Admin: Pierre Lindenbaum

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France/Nantes/Institut du Thorax - INSERM UMR1087
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Posts by Pierre Lindenbaum

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Comment: C: changing of chromosome notation in CHROM columns of vcf file
... Hello aarvaBioinfo! Questions similar to yours can already be found at: Replacing the Chr names and position notions in vcf Changing Chromosome Notation On Vcf Human dna reference file with no prefix 'chr' VCF files: Change Chromosome Notation Change chromosome notation to match a ...
written 2 days ago by Pierre Lindenbaum108k
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Answer: A: GATK UnifiedGenotyper doesn't output the variants in vcf files
... > -gt_mode GENOTYPE_GIVEN_ALLELES Specifies how to determine the alternate alleles to use for genotyping > --alleles / -alleles Set of alleles to use in genotyping When --genotyping_mode is set to GENOTYPE_GIVEN_ALLELES mode, the caller will genotype the samples using only the alleles provide ...
written 3 days ago by Pierre Lindenbaum108k
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Answer: A: Filtering reads on the basis of percentage of ambiguous(N's) characters
... using paste + awk: gunzip -c input.fq.gz |\ paste - - - - |\ awk -F '\t' '{S=$2;L=1.0*length(S);gsub(/[^ATGCatgc]/,"",S);L2=length(S); if(L2/L > 0.05) print $0;}' |\ tr "\t" "\n" ...
written 3 days ago by Pierre Lindenbaum108k
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Comment: C: Is it practical to trap miRNA using PCR?
... how is it related to bioinformatics ? ...
written 4 days ago by Pierre Lindenbaum108k
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Comment: C: A function for having a multiway intersection
... [DON'T SHOUT PLEASE.][1] [1]: https://newrepublic.com/article/117390/netiquette-capitalization-how-caps-became-code-yelling ...
written 4 days ago by Pierre Lindenbaum108k
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Comment: C: A function for having a multiway intersection
... Hello jivarajivaraj! It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/4533 This is typically not recommended as it runs the risk of annoying people in both communities. ...
written 4 days ago by Pierre Lindenbaum108k
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Comment: C: Get variant position knowing the gene name, base change, and NM#
... see https://www.biostars.org/p/15992/ ; ...
written 4 days ago by Pierre Lindenbaum108k
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Answer: A: Issue with Bcftools reheader
... the option -s of bcftools reheader is a **FILE** not a string. https://samtools.github.io/bcftools/bcftools.html -s, --samples FILE new sample names, one name per line, in the same order as they appear in the VCF file. Alternatively, only samples which need to be renamed can be listed ...
written 5 days ago by Pierre Lindenbaum108k
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Comment: C: Software to calculate frequency of mutation by group
... If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted. ![Upvote|Bookmark|Accept][1] [1]: http://i68.tinypic.com/2m2ykjr.png ...
written 5 days ago by Pierre Lindenbaum108k
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Comment: C: GATK3 error message
... > your data is corrupted try to understand what I've done in my previous comment please https://www.biostars.org/p/321787/#321805 ...
written 5 days ago by Pierre Lindenbaum108k

Latest awards to Pierre Lindenbaum

Teacher 1 hour ago, created an answer with at least 3 up-votes. For A: Getting A Vcf File From A Fasta Alignment
Scholar 1 hour ago, created an answer that has been accepted. For A: How One Can Separate Noncoding From Coding Ucsc And Ensembl Transcripts
Teacher 6 hours ago, created an answer with at least 3 up-votes. For A: Getting A Vcf File From A Fasta Alignment
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: Getting A Vcf File From A Fasta Alignment
Appreciated 5 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: Extracting List Of Genes Associated With A Pathway In Kegg
Scholar 5 days ago, created an answer that has been accepted. For A: How Complex It Is To Analyze Ngs Data ?
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: Extracting List Of Genes Associated With A Pathway In Kegg
Scholar 5 days ago, created an answer that has been accepted. For A: How Complex It Is To Analyze Ngs Data ?
Teacher 7 days ago, created an answer with at least 3 up-votes. For A: Extracting List Of Genes Associated With A Pathway In Kegg
Scholar 7 days ago, created an answer that has been accepted. For A: How Complex It Is To Analyze Ngs Data ?
Appreciated 11 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Scholar 12 days ago, created an answer that has been accepted. For A: How Complex It Is To Analyze Ngs Data ?
Scholar 15 days ago, created an answer that has been accepted. For A: When Hard clipping is used instead of the Soft clipping ?
Scholar 15 days ago, created an answer that has been accepted. For A: Error in samtools view
Teacher 15 days ago, created an answer with at least 3 up-votes. For A: How To Extract Snps From A Desired List Of Gene Names
Scholar 15 days ago, created an answer that has been accepted. For A: Error in samtools view
Scholar 16 days ago, created an answer that has been accepted. For A: Error in samtools view
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: How To Extract Snps From A Desired List Of Gene Names
Scholar 16 days ago, created an answer that has been accepted. For A: Error in samtools view
Popular Question 17 days ago, created a question with more than 1,000 views. For samtools 1.0 'index' : CSI index vs BAI index ?
Scholar 18 days ago, created an answer that has been accepted. For A: Error in samtools view
Scholar 21 days ago, created an answer that has been accepted. For A: Error in samtools view

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